I can't see how the AFL could prevent it. Players take pay cuts in order to change clubs all the time. Integrity of SC? On what grounds? Again, provided that the player, his current club and his incumbent club are all in agreement to the trade and his incumbent club is able to fit whatever salary is agreed upon into their SC then there is nothing that the AFL can or will do.
As far as GAJ threatening to retire goes, he could just be telling the truth but I highly doubt that.

I also believe that it has nothing to do with the AFL though. I think that it has more to do with the Suns and their potential unwillingness to let him go. Now they're not going to get a great deal as far as compensation goes but something that could be worth quite a bit to them is being able to get rid of his million dollar salary, or even a massive portion of it. As I'm sure you would already know, if GAJ decides to retire although the Suns won't have to pay him a cent his salary must still have to be included in their TPP. It would be an unmitigated disaster if the Suns still had GAJ's salary tied up in their cap in 2018 and he was no longer playing for them (retired). This is where GAJ's leverage is and he's already using it to his advantage.